proteins one lecture talking about secondary structure so certain areas of a Ramachandran plot are labeled with the name of a particular regular secondary structure and these are things you may have heard of regular just means repeating Phi psy angles and so for example anti parallel beta sheets parallel beta sheets right-handed alpha helix etc you do need to know these Phi site combinations which I have listed here for two types of secondary structure the alpha helix and the beta strand these are two types of regular secondary structure I'll define that later so an alpha helix for example is minus 60 degrees minus 45 degrees which here if you look on the x-axis minus 60 you come down from 0 to minus 45 you have this region it's an allowed region and that's where you would typically find an alpha helix a beta strand I say is typically minus 150 plus 150 which is sort of like Yellowstone National Park in Wyoming if you know that reference the other regions we're not going to focus on as much this is what the Ramachandran plot looks like for an actual protein this is a structure that was determined by x-ray crystallography for a protein I don't know what it is but you can access that in the protein databank with the PDB code 2 GBP notice that there's one dot for every amino acid residue so it looks like there are no maybe a couple hundred or more amino acids in this protein the green contours are statistical probabilities that I was describing like the allowed and generously allowed regions and you should notice that most but not all of the dots lie inside the allowed regions every residue with regular or irregular which means not repeating Phi sized structures will have a dot and that means that the protein structure is relatively fixed in space and time what are not shown in this plot our glycine residues and proline residues and and that's because glycine has an additional allowed region because it has no side chain it's a quite a bit more flexible it can adopt different confirmations compared to other amino acids prolene is not shown here because of its five membered ring structure the Phi angle is fixed at minus 60 so it would be always any proteins would always lie on this line here so it has that extra constraint in fact every amino acid has its own green contour region and they're they're all a little bit different and you can google those if you're interested so let's now go into secondary structure specific types we have regular secondary structure we have irregular and we have random coil they're all defined by their backbone structure which means dihedral angles Phi n sy and their interactions so regular secondary structure means repeating Phi sy pairs and it gives rise to structures like a beta strand or an alpha helix these structures are stable and that means they don't change over time and I say dramatically because there's always some flexibility in these molecules but there's some small range of angles in which you would find any given amino acid so we're just going to call them stable meaning there's a single Phi Sai angle their backbone NH donors and carbonyls acceptors are involved in hydrogen bonds so they're NHS are donating a hydrogen bond and the CE OS are accepting hydrogen bond and the key is that they're donating and accepting to and from neighboring backbone atoms so in the example of the Alpha helix it would be a carbonyl bonded to an NH on the successive rung of the helix but uh the other kind of beta strand has a bit different pattern and we'll get into that later irregular secondary structure means non-repeating phi Sai pairs and so that means that the backbone doesn't give rise to something that's all straight or all coiled but it might go on different kinds of directions for each amino acid however these structures are still stable and they're unchanging and they have their backbone hydrogen bond donors and acceptors still interacting with nearby functional groups of the protein and that could be other backbone atoms or other side chains but the donors and acceptors of this backbone of a non-repeating irregular structure will still be all of them in hydrogen bombs with the protein finally we have random coil structure which actually changes over time so there is no Feist I defined combination for any given residue because the backbone is dynamic the only hydrogen bonds here are from the NHS and the COS to water not the protein and so these are basically not anchored to the protein and they're undergo a lot of conformational changes so let's take an example of regular secondary structure the Alpha helix where again - 60-45 is the definition of the Phi Phi angle it has three point six residues per turn of the helix and so that means that you have what does that mean 360 degrees per turn of course so that's a hundred and a hundred degrees of turn for every amino acid the pitch is five point four angstroms which I generally just ignore all the carbonyls on residue n are hydrogen bonded to all n H's on the next turn which is the residue n plus four so if you look at this amino acid here the carbonyl that's the seat the C the NH is not shown C alpha C O so that Co of residue n let's count up plus four residues and we should get to the NH on the next ring so here's the NH n plus one there's the NH n plus two there's the NH on plus three and here's the NH on plus four so if this was amino acid one this is amino acid five so that NH points back at the n-terminus of the helix and the carbonyl points up here at the c-terminus of the helix and the hydrogen bond itself is in parallel with the helical axis and alpha helix is unique in its structure that the core is tightly packed with all the atoms at vanderwaal's distance there are no gaps for water if we had more than 3.6 residues per turn there would be a hole down the middle of the helix and if it was less than 3.6 residues per turn there would be gaps between the rungs and the pitch would have to increase but this particular arrangement to the alpha helical arrangement actually represents the smallest possible volume for the atoms to occupy which has important implications for protein folding and stability there's another picture of the Alpha helix where you can see in yellow the side chains point straight out from the the helical axis like a bottle brush or a mongoose tail beta sheet is shown here it has minus 150 plus 150 it also utilizes the full hydrogen bonding capacity of the backbone the regular minus 151 plus 150 gives it an extended conformation 180 180 is not actually possible because the let's see that would be completely extended and you can easily draw this in the in a piece of paper but that would put the side chains at on neighboring strands pointed directly at the neighboring polypeptide and it would give a steric clash but if you rotate the side chain away from the plane then you get these pleats and so that's how we get minus 150 plus 150 the strands here can be shown in a parallel direction where the the sequences go from n to C terminus in the same direction or anti parallel which is more common and more stable again I've given you the observed Phi Sai every other side chain points up so on the left side of this sheet you can see here are the red no where they here are the purple groups pointing left this one points left and then the two amino acids away again left and left two amino acids away left and left with the intervening ones pointing to the right side of the sheet the pleats actually gives a good a better geometry for the carbonyl hydrogen bond with the NH and you can see that this NH here is is hydrogen bonded to the neighboring strand carbonyl and then on the next carbonyl it's bonded to the NH etc so all of the backbone NHS are in hydrogen bonds with carbonyls on neighboring backbones here's another drawing of an anti-parallel orientation where you can actually this is the C the NH the C alpha the co NH C alpha C oh so n to C Direction goes to the right and then it could wrap around and go back to the left on the anti parallel strand there are two types of non repetitive or irregular protein structure and the right is called an Omega loop and to me it just looks like a colon or something but it just shows you that it doesn't look like an alpha helix on the left is a pretty common kind of structural feature called a type 2 beta turn so between strands of a beta sheet if this is the strand coming from the right over to the C you want the C alpha for a residue one residue 2 residue 3 residue 4 and then it's turned around and can go back to the right in an anti parallel strand in this case the the first and fourth residues in the turn have a hydrogen bond and there's a particular Phi site combination for residues two and three in this residue 2 is often prolene because the minus 60 degree Phi angle actually positions this bond to be in a turn like confirmation residue 3 is really often with a glycine because without an R group here it relieves some steric clash with the second positions carbonyl you don't need to know these details but I'm just showing you that prolene and glycine don't typically fall in the Phi Sai combinations that are nice for alpha helixes or beta strands but they're often found in turn regions you can look at a table of propensity zuv amino acid residues for alpha helical or beta sheet confirmations it's hard to make heads or tails of this but you'll notice that glycine for example is not often found it has a low propensity to be found in alpha helixes and that's about the only thing you can say from this table so you can pretty much ignore it and that's it for secondary structure and module 5 the rest of the protein structure will come after your exam